Semiparametric multiple QTL mapping method where
the non-genetic covariate effects are modeled
nonparametrically.
The software and the related paper
can be downloaded. Detailed user manual will be posted soon.

HapSample is a web
application for
simulating SNP genotypes for case-control and affected-child trio studies by
resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs
to be "genotyped," along with a disease model file that describes causal SNPs
and their effect sizes. The simulation tool is appropriate for candidate
regions or whole-genome scans. A command line version is also available
here .

Bias correction in genome scans. R code
and an Excel calculator are available
here . The paper
can be downloaded here .

The software,
ShrunkenPCA,
implements the shrunken principal component analysis that automatically
accounts for genomic correlation structure among SNPs.
ShrunkenPCA is compatible with the most popular stratification analysis
tool,
EigenSoft .